<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
<html><head><title></title>
<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
<link rel="stylesheet" type="text/css" href="search.css"/>
<script type="text/javascript" src="search.js"></script>
</head>
<body class="SRPage">
<div id="SRIndex">
<div class="SRStatus" id="Loading">Loading...</div>
<div class="SRResult" id="SR_chain">
 <div class="SREntry">
  <a id="Item0" onkeydown="return searchResults.Nav(event,0)" onkeypress="return searchResults.Nav(event,0)" onkeyup="return searchResults.Nav(event,0)" class="SRSymbol" href="javascript:searchResults.Toggle('SR_chain')">Chain</a>
  <div class="SRChildren">
    <a id="Item0_c0" onkeydown="return searchResults.NavChild(event,0,0)" onkeypress="return searchResults.NavChild(event,0,0)" onkeyup="return searchResults.NavChild(event,0,0)" class="SRScope" href="../classmoltk_1_1PDBStructure_1_1Chain.html#acbbbb6eba40ef9cd1ac8123ca4bbd453" target="_parent">moltk::PDBStructure::Chain::Chain()</a>
    <a id="Item0_c1" onkeydown="return searchResults.NavChild(event,0,1)" onkeypress="return searchResults.NavChild(event,0,1)" onkeyup="return searchResults.NavChild(event,0,1)" class="SRScope" href="../classmoltk_1_1PDBStructure_1_1Chain.html#a08a5fd5b7db7c07432c777b69a6467ce" target="_parent">moltk::PDBStructure::Chain::Chain(const Chain &amp;rhs)</a>
  </div>
 </div>
</div>
<div class="SRResult" id="SR_clear_5fpositions">
 <div class="SREntry">
  <a id="Item1" onkeydown="return searchResults.Nav(event,1)" onkeypress="return searchResults.Nav(event,1)" onkeyup="return searchResults.Nav(event,1)" class="SRSymbol" href="../classmoltk_1_1Aligner.html#a729b4f44dd7e0411b0acdde5c1561af5" target="_parent">clear_positions</a>
  <span class="SRScope">moltk::Aligner</span>
 </div>
</div>
<div class="SRResult" id="SR_clear_5fscorer">
 <div class="SREntry">
  <a id="Item2" onkeydown="return searchResults.Nav(event,2)" onkeypress="return searchResults.Nav(event,2)" onkeyup="return searchResults.Nav(event,2)" class="SRSymbol" href="../classmoltk_1_1Aligner.html#ace84085990dcff6eac7f8baf8a5c5d9a" target="_parent">clear_scorer</a>
  <span class="SRScope">moltk::Aligner</span>
 </div>
</div>
<div class="SRResult" id="SR_clone">
 <div class="SREntry">
  <a id="Item3" onkeydown="return searchResults.Nav(event,3)" onkeypress="return searchResults.Nav(event,3)" onkeyup="return searchResults.Nav(event,3)" class="SRSymbol" href="javascript:searchResults.Toggle('SR_clone')">clone</a>
  <div class="SRChildren">
    <a id="Item3_c0" onkeydown="return searchResults.NavChild(event,3,0)" onkeypress="return searchResults.NavChild(event,3,0)" onkeyup="return searchResults.NavChild(event,3,0)" class="SRScope" href="../classmoltk_1_1Aligner_1_1QueryPosition.html#a64031ae54838bdf696af90538b4adec9" target="_parent">moltk::Aligner::QueryPosition::clone()</a>
    <a id="Item3_c1" onkeydown="return searchResults.NavChild(event,3,1)" onkeypress="return searchResults.NavChild(event,3,1)" onkeyup="return searchResults.NavChild(event,3,1)" class="SRScope" href="../classmoltk_1_1Aligner_1_1TargetPosition.html#a435ce934a271909290d859e2e7375984" target="_parent">moltk::Aligner::TargetPosition::clone()</a>
    <a id="Item3_c2" onkeydown="return searchResults.NavChild(event,3,2)" onkeypress="return searchResults.NavChild(event,3,2)" onkeyup="return searchResults.NavChild(event,3,2)" class="SRScope" href="../classmoltk_1_1MatrixScorer_1_1QueryPosition.html#a4db8009ff73af91086b6a00931d43ba6" target="_parent">moltk::MatrixScorer::QueryPosition::clone()</a>
    <a id="Item3_c3" onkeydown="return searchResults.NavChild(event,3,3)" onkeypress="return searchResults.NavChild(event,3,3)" onkeyup="return searchResults.NavChild(event,3,3)" class="SRScope" href="../classmoltk_1_1MatrixScorer_1_1TargetPosition.html#a283dedf30a28c62172f99c864fdb8dad" target="_parent">moltk::MatrixScorer::TargetPosition::clone()</a>
  </div>
 </div>
</div>
<div class="SRResult" id="SR_compute_5fcell_5frecurrence">
 <div class="SREntry">
  <a id="Item4" onkeydown="return searchResults.Nav(event,4)" onkeypress="return searchResults.Nav(event,4)" onkeyup="return searchResults.Nav(event,4)" class="SRSymbol" href="../classmoltk_1_1Aligner.html#a38863ca0eb76e0241abedefaa69b0048" target="_parent">compute_cell_recurrence</a>
  <span class="SRScope">moltk::Aligner</span>
 </div>
</div>
<div class="SRResult" id="SR_compute_5fcell_5frecurrence_5ffreee">
 <div class="SREntry">
  <a id="Item5" onkeydown="return searchResults.Nav(event,5)" onkeypress="return searchResults.Nav(event,5)" onkeyup="return searchResults.Nav(event,5)" class="SRSymbol" href="../classmoltk_1_1Aligner.html#a5c0dfb557f1fe73f8b0b6dc6eb029ab2" target="_parent">compute_cell_recurrence_freeE</a>
  <span class="SRScope">moltk::Aligner</span>
 </div>
</div>
<div class="SRResult" id="SR_compute_5fcell_5frecurrence_5ffreeef">
 <div class="SREntry">
  <a id="Item6" onkeydown="return searchResults.Nav(event,6)" onkeypress="return searchResults.Nav(event,6)" onkeyup="return searchResults.Nav(event,6)" class="SRSymbol" href="../classmoltk_1_1Aligner.html#a8d28c9bb018c6d4913e305c36093eeb0" target="_parent">compute_cell_recurrence_freeEF</a>
  <span class="SRScope">moltk::Aligner</span>
 </div>
</div>
<div class="SRResult" id="SR_compute_5fcell_5frecurrence_5ffreef">
 <div class="SREntry">
  <a id="Item7" onkeydown="return searchResults.Nav(event,7)" onkeypress="return searchResults.Nav(event,7)" onkeyup="return searchResults.Nav(event,7)" class="SRSymbol" href="../classmoltk_1_1Aligner.html#ac1c097af307968d9caf76242977a288d" target="_parent">compute_cell_recurrence_freeF</a>
  <span class="SRScope">moltk::Aligner</span>
 </div>
</div>
<div class="SRResult" id="SR_compute_5frecurrence">
 <div class="SREntry">
  <a id="Item8" onkeydown="return searchResults.Nav(event,8)" onkeypress="return searchResults.Nav(event,8)" onkeyup="return searchResults.Nav(event,8)" class="SRSymbol" href="../classmoltk_1_1Aligner.html#a66756b5e61b63ee8f26b6abb7b1de02e" target="_parent">compute_recurrence</a>
  <span class="SRScope">moltk::Aligner</span>
 </div>
</div>
<div class="SRResult" id="SR_compute_5ftraceback">
 <div class="SREntry">
  <a id="Item9" onkeydown="return searchResults.Nav(event,9)" onkeypress="return searchResults.Nav(event,9)" onkeyup="return searchResults.Nav(event,9)" class="SRSymbol" href="../classmoltk_1_1Aligner.html#ac6170833b8d8c742719e45186aff85b8" target="_parent">compute_traceback</a>
  <span class="SRScope">moltk::Aligner</span>
 </div>
</div>
<div class="SRResult" id="SR_compute_5ftraceback_5fpointer">
 <div class="SREntry">
  <a id="Item10" onkeydown="return searchResults.Nav(event,10)" onkeypress="return searchResults.Nav(event,10)" onkeyup="return searchResults.Nav(event,10)" class="SRSymbol" href="../classmoltk_1_1Aligner_1_1Cell.html#a46afa907bfe05f49dec3a49ec22cb9ef" target="_parent">compute_traceback_pointer</a>
  <span class="SRScope">moltk::Aligner::Cell</span>
 </div>
</div>
<div class="SRResult" id="SR_compute_5fv">
 <div class="SREntry">
  <a id="Item11" onkeydown="return searchResults.Nav(event,11)" onkeypress="return searchResults.Nav(event,11)" onkeyup="return searchResults.Nav(event,11)" class="SRSymbol" href="../classmoltk_1_1Aligner_1_1Cell.html#ad8b6f514f6420389c670370687518fb4" target="_parent">compute_v</a>
  <span class="SRScope">moltk::Aligner::Cell</span>
 </div>
</div>
<div class="SRResult" id="SR_const_5fiterator">
 <div class="SREntry">
  <a id="Item12" onkeydown="return searchResults.Nav(event,12)" onkeypress="return searchResults.Nav(event,12)" onkeyup="return searchResults.Nav(event,12)" class="SRSymbol" href="javascript:searchResults.Toggle('SR_const_5fiterator')">const_iterator</a>
  <div class="SRChildren">
    <a id="Item12_c0" onkeydown="return searchResults.NavChild(event,12,0)" onkeypress="return searchResults.NavChild(event,12,0)" onkeyup="return searchResults.NavChild(event,12,0)" class="SRScope" href="../classmoltk_1_1EString_1_1const__iterator.html#a01ca7c5f3f2ebebee963d591ba185353" target="_parent">moltk::EString::const_iterator::const_iterator()</a>
    <a id="Item12_c1" onkeydown="return searchResults.NavChild(event,12,1)" onkeypress="return searchResults.NavChild(event,12,1)" onkeyup="return searchResults.NavChild(event,12,1)" class="SRScope" href="../classmoltk_1_1EString_1_1const__iterator.html#a1b4b8a315d0b2d1748f1e710ec6adc98" target="_parent">moltk::EString::const_iterator::const_iterator(const std::vector&lt; int &gt; &amp;runs, int run_index, int position_index)</a>
  </div>
 </div>
</div>
<div class="SRResult" id="SR_cos">
 <div class="SREntry">
  <a id="Item13" onkeydown="return searchResults.Nav(event,13)" onkeypress="return searchResults.Nav(event,13)" onkeyup="return searchResults.Nav(event,13)" class="SRSymbol" href="../namespacemoltk_1_1units.html#aee4bd73aa460f5124d4025406ead2998" target="_parent">cos</a>
  <span class="SRScope">moltk::units</span>
 </div>
</div>
<div class="SRResult" id="SR_create_5ffoo_5fpositions">
 <div class="SREntry">
  <a id="Item14" onkeydown="return searchResults.Nav(event,14)" onkeypress="return searchResults.Nav(event,14)" onkeyup="return searchResults.Nav(event,14)" class="SRSymbol" href="../classmoltk_1_1MatrixScorer.html#aef587746f1419b9b985ee68ff1455f04" target="_parent">create_foo_positions</a>
  <span class="SRScope">moltk::MatrixScorer</span>
 </div>
</div>
<div class="SRResult" id="SR_create_5fquery_5fpositions">
 <div class="SREntry">
  <a id="Item15" onkeydown="return searchResults.Nav(event,15)" onkeypress="return searchResults.Nav(event,15)" onkeyup="return searchResults.Nav(event,15)" class="SRSymbol" href="javascript:searchResults.Toggle('SR_create_5fquery_5fpositions')">create_query_positions</a>
  <div class="SRChildren">
    <a id="Item15_c0" onkeydown="return searchResults.NavChild(event,15,0)" onkeypress="return searchResults.NavChild(event,15,0)" onkeyup="return searchResults.NavChild(event,15,0)" class="SRScope" href="../classmoltk_1_1Aligner_1_1Scorer.html#a090273ed5beeae79b7058f647a863d84" target="_parent">moltk::Aligner::Scorer::create_query_positions()</a>
    <a id="Item15_c1" onkeydown="return searchResults.NavChild(event,15,1)" onkeypress="return searchResults.NavChild(event,15,1)" onkeyup="return searchResults.NavChild(event,15,1)" class="SRScope" href="../classmoltk_1_1MatrixScorer.html#a6732a8098d7e4811669934618d5ea1ef" target="_parent">moltk::MatrixScorer::create_query_positions()</a>
  </div>
 </div>
</div>
<div class="SRResult" id="SR_create_5ftarget_5fpositions">
 <div class="SREntry">
  <a id="Item16" onkeydown="return searchResults.Nav(event,16)" onkeypress="return searchResults.Nav(event,16)" onkeyup="return searchResults.Nav(event,16)" class="SRSymbol" href="javascript:searchResults.Toggle('SR_create_5ftarget_5fpositions')">create_target_positions</a>
  <div class="SRChildren">
    <a id="Item16_c0" onkeydown="return searchResults.NavChild(event,16,0)" onkeypress="return searchResults.NavChild(event,16,0)" onkeyup="return searchResults.NavChild(event,16,0)" class="SRScope" href="../classmoltk_1_1Aligner_1_1Scorer.html#ac699ce5b5c5eb5d06d7875ae3bc6e881" target="_parent">moltk::Aligner::Scorer::create_target_positions()</a>
    <a id="Item16_c1" onkeydown="return searchResults.NavChild(event,16,1)" onkeypress="return searchResults.NavChild(event,16,1)" onkeyup="return searchResults.NavChild(event,16,1)" class="SRScope" href="../classmoltk_1_1MatrixScorer.html#adadccdab70f7531e88e619a75dcf58c7" target="_parent">moltk::MatrixScorer::create_target_positions()</a>
  </div>
 </div>
</div>
<div class="SRStatus" id="Searching">Searching...</div>
<div class="SRStatus" id="NoMatches">No Matches</div>
<script type="text/javascript"><!--
document.getElementById("Loading").style.display="none";
document.getElementById("NoMatches").style.display="none";
var searchResults = new SearchResults("searchResults");
searchResults.Search();
--></script>
</div>
</body>
</html>
